[gmx-users] problem with energy minimization

[Mark Abraham]

On 31/01/2012 6:05 PM, Emanuel Birru wrote:
> Yeah, Tsjerk is is right, it seems you are using 4 cpu and your system 
> is too small to run in on more than one node (CPU).

If you look at the minimum required DD cell size reported by mdrun, it 
is much too large (~4nm). It is quite likely that there is problem other 
than simulation cell size.

Mark

> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] 
> on behalf of Tsjerk Wassenaar [tsjerkw at gmail.com]
> *Sent:* Tuesday, January 31, 2012 5:58 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] problem with energy minimization
>
> Hi Anushree,
>
> You're not using a single cpu, although you probably think you do. Is 
> this em in vacuum or just a small system? Either way, you can enforce 
> running on a single cpu by adding '-nt 1' to the mdrun options.
>
> Cheers,
>
> Tsjerk
>
>> On Jan 31, 2012 7:53 AM, "Anushree Tripathi" 
>> <anushritripathi at gmail.com <mailto:anushritripathi at gmail.com>> wrote:
>>
>> I am using single CPU for this simulation.
>>
>> On Tue, Jan 31, 2012 at 11:09 AM, Emanuel Birru 
>> <Emanuel.Birru at monash.edu <mailto:Emanuel.Birru at monash.edu>> wrote:
>>
>>     > > > > From: gmx-users-bounces at gromacs.org
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